Tuesday, August 31, 2010

They say that the best way to learn something is to teach it. Anne McNeil and her colleagues from the University of Michigan have taken that aphorism to heart by assigning students the task of creating and editingWikipedia entries.

McNeil’s graduate students in Chemistry and Macromolecular Science and Engineering work with some extremely complicated concepts. If they could communicate the material clearly to the general public, this would both improve the students’ understanding as well as provide a service to interested lay people.

Working in small teams, the students chose graduate level chemistry topics that were not already adequately covered by Wikipedia and set out to improve them. Their task was to create accurate, readable entries. Not surprisingly, the students evaluated the project very highly as a teaching tool. The project worked so well, that McNeil now plans to assign undergraduates the task of editing entries on famous chemists and chemical reactions.

When McNeil first assigned the Wikipedia project in 2008, she and her students had to learn how Wikipedia works. Since then, she and her graduate student instructor Cheryl Moy have written a handbook on editing Wikipedia chemistry entries. In May, McNeil and Moy were invited to Wikimedia Foundation headquarters in San Francisco to give a presentation on using Wikipedia as a teaching tool.

If you are interested in editing or creating a Wikipedia article, here are some basic instructions and the Wikipedia editing policy.

Salama and her team identified four genes responsible for creating the typical helical shape of H. pylori. These proteins snip the bacterial cell wall in strategic places, allowing the stiff rod-shaped cell wall to twist into a helix. Mutants lacking any one of the genes were unable to twist into proper shapes, and more importantly, were unable to colonize mouse stomachs.

At first, the researchers assumed that the mutant bacteria were having trouble pushing their way through the thick gelatin-like mucus that coats stomachs. However, the odd-shaped bugs had no trouble propelling themselves through comparable amounts of gel in Petri dishes. It is unclear why the twisted shape is critical for infection. In any case, microbiologists hope to use the shape-changing genes as drug targets, especially as several other disease-causing pathogens, such as Vibrio cholerae (cholera), and Campylobacter jejuni (bacterial diarrhea) have the same proteins.

Sunday, August 29, 2010

Astronomers from NASA, the SETI Institute, the Smithsonian Institution and various universities have discovered evidence that the moon is contracting. The researchers used images from NASA’s Lunar Reconnaissance Orbiter (LRO) to draw their conclusions.

The images revealed a series of lunar cliffs, known as lobate scarps (lobe-shaped cliffs). Although some of these scarps were first discovered during the Apollo missions in the 70’s, at that time, instrumentation only allowed for photographing near the lunar equator. In contrast, the LRO has found the scarps scattered across the lunar surface, indicating that they are a moonwide phenomenon.

Just as mountains on Earth are caused by the movements of tectonic plates, so too are lunar cliffs caused by the contraction of the lunar surface. This isn’t so surprising. Scientists have long thought that the moon, which was created as the red-hot result of a massive collision, would have shrunk as it cooled. And indeed, estimates are that over the past four billion years, the moon has shrunk by about 600 feet in diameter. The interesting thing is that many of the scarps created by the contracting process cut across small, and thus relatively short-lived, craters. This means that some of the scarps may only be a hundred million years old or younger, evidence that the shrinking process is still underway.

A fault cuts across and deforms several small diameter (~40-m diameter) impact craters (arrows). About half of the rim and floor of a 20 m-in-diameter crater shown in the box has been lost. Since small craters only have a limited lifetime before they are destroyed by newer impacts, their deformation by the fault shows the fault to be relatively young.

Saturday, August 28, 2010

Acetaminophen, the active ingredient in Tylenol, is a well-known over-the-counter pain reliever. Surprisingly, a Psychological Science study by University of Florida psychologist Gregory Webster shows that it can heal social pains as well.

Webster gave 24 women and 6 men 500 mg of acetaminophen twice a day for three weeks (upon waking and before bed), and gave another 24 women and 8 men a placebo. Neither group knew what they were taking. The acetaminophen group self-reported significantly fewer hurt feelings than the placebo group during the three week period.

Functional magnetic resonance imaging (fMRI) corroborated these results. While hooked up to the fMRI machine, participants were asked to play a computer game in which their avatar is suddenly and inexplicably excluded from a ball game with two other partners. The acetaminophen users showed less activity in regions of the brain associated with emotional processing.

Overdosing on acetaminophen can have serious consequences, such as liver failure. Webster cautions that until more research is done, people should not take acetaminophen to cope with personal slights. If acetaminophen does prove to be effective for this purpose, it could be a relatively safe, mild alternative to more powerful drugs.

Friday, August 27, 2010

Until recently, it was thought that for men to build muscle mass, they had to lift extremely heavy weights. Nicholas Burd from McMaster University was lead author in a study disproving this. It’s muscle fatigue, not heavy weight lifting that leads to muscle growth. In other words, lifting a lighter weight many times was more effective at building muscle mass than lifting a heavy weight a few times.

Burd and his team put 15 men through their weight lifting paces. The men were asked to lift either 90% of their maximum ability (a typical amount for men seeking to increase muscle mass) or only 30%. For the 90% weights, the men lifted the weight until ‘failure’, when they could no longer complete the full range of motion. The 30% weights were either lifted to achieve an equal amount of work (load times repetition) as was done with the 90% weights, or was done to failure. Muscle biopsies were done 4 and 24 hours after lifting the weights. Lifting the 30% weights to failure led to the greatest increase in muscle mass.

Interestingly, the total amount of work done was significantly higher in the ‘30% to failure’ group. Apparently, the men were able to push themselves to do more repetitions and ultimately lift more total weight when each load was lighter. That makes me wonder whether the true secret to gaining muscle mass is simply to move the highest total amount of weight at each session. Starting with a lower weight per repetition lets people get to a higher total weight amount than they could achieve if they started with a heavier weight.

Wednesday, August 25, 2010

Moshe Gish, Amots Dafni and Moshe Inbar of the University of Haifa have uncovered a defense mechanism insects use to avoid being eaten by herbivores. Apparently, they can detect animal breath.

You might wonder why insects need to escape from plant-eating mammals. After all, herbivores have no interest in insects, only in leaves. The point is that many tiny insects, such as the 2 to 4 mm long pea aphids used in this study, live relatively sedentary lives on one or a few leaves. When a large animal tries to make a meal of that leaf, it can gobble up the aphids along with the leaf unless they make an escape. It turns out that aphids are remarkably good at knowing when to drop off a leaf just before it disappears down an animal’s gullet.

After determining that it was the animals’ breath that was triggering the aphids to launch themselves off leaves rather than noises, vibrations, shadows or other cues, the researchers set about determining what component of breath was responsible. At this stage of the experimentation, they began to use snorkels to direct their own breaths away from the aphid-infested plants.

At first, the scientists expected to find that carbon dioxide or some other chemical component of the breath was responsible. They found that the answer was much simpler. It was the combination of warmth and humidity in the exhaled breath that caused the aphids to drop from the leaves. The researchers predict that other invertebrates will be found that use the same defense cues.

Tuesday, August 24, 2010

Briefly, cavitation is the process whereby collapsing bubbles create shock waves. Usually, these waves radiate out in all directions and cannot be tightly controlled. Zhong and his team got the idea of using two bubbles in tandem to direct the energy flow in a specific direction, namely to puncture and inject a nearby cell.

The team used lasers to precisely create tiny bubbles of blue dye within a liquid surrounding a target cell. First, one bubble is created and allowed to expand. Exactly at the point when that bubble would normally collapse, a second bubble is created. The expansion of the second bubble puts pressure on the first. Instead of dissipating in a radial fashion, the first bubble now accelerates toward the cell, puncturing it and injecting it with the blue dye.

The timed expansion and collapse of two bubbles creates a liquid jet that can penetrate a fine hole in the membrane of a cell. From left to right: A laser (green circle) focused inside a water bath locally vaporizes the liquid, creating an expanding bubble (light blue). Just after the first bubble reaches its maximum size, a second laser (red circle) generates another bubble. As the second bubble expands and the first bubble collapses, a rush of liquid forms along the vertical line between the two, creating a high-speed liquid jet that accelerates toward the cell with enough force to penetrate the membrane.

Credit: Alan Stonebraker, American Physical Society

The mammalian cells that the researchers used have membranes that are impervious to the blue dye unless they are first perforated. The clear evidence of blue dye within the cells indicates that the bubble technique was successful. Unfortunately, the toxic blue dye also happened to kill the cells. Hopefully, that won’t be the case with any therapeutic agents that are injected in this manner. The ability to deliver drugs to specific cells is expected to be an especially useful tool for scientists working with stem cells.

Monday, August 23, 2010

Archeologists not only dig up artifacts, but also try to determine as much as possible about what they are, when and how they were made, who used them, and anything else they can find out. Unfortunately, the process of answering many of these questions has required destroying small chips of the material. The fragments are subjected to various types of analysis to determine exact composition. Yuval Goren of Tel Aviv University may have changed all that.

Goren uses x-ray fluorescence (XRF) to analyze the chemical composition of artifacts such as clay tablets, coins, or glass without damaging them. By comparing his data with data collected over the years from more destructive sampling, he has compiled a table of times and locations of manufacture. For example, Goren was recently able to determine the origin and possibly the sender of a 3500 year-old letter.

The XRF device can be used either in the lab or in the field. As fewer and fewer museums are allowing traditional, destructive analysis of items in their collections, Goren predicts that his method is going to be in great demand. He intends to make it available to anyone who wishes to use it.

Sunday, August 22, 2010

Thomas Weiss from the Friedrich-Schiller-University Jena and his team have developed a hand prosthesis that they hope will eliminate phantom hand pain.

Phantom pain is the phenomenon in which a person feels persistent pain or itching coming from a limb that has been amputated. Sufferers will sometimes insist that the missing hand or foot is extremely painful to them. Understandably, this has been difficult for physicians to treat, since there is no hand or foot. Painkillers can be ineffective, and the discomfort can last years or even a lifetime.

At first, phantom pain was thought to be triggered by crushed or damaged nerves at the amputation site. Now, it is known that the discomfort originates directly in the brain. The part of the brain responsible for the missing limb now has no job, and begins to fire when other parts of the body are stimulated. In some cases, stroking part of a patient’s face will create the sensation of touching a missing limb.

Weiss’s idea was to create a prosthesis that sends precise sensory information from pressure sensors in an artificial hand to nerves in the upper arm. Hopefully, the brain will interpret the sensations as originating in the prosthetic hand, just as it would from a real hand. This should give the hand-control part of the brain its job back, preventing the re-organization of the brain that causes the phantom limb pain.

So far, the device has been tested on only a few patients, but with promising results.

The new development from Jena provides the upper arm with sensory information which is then transmitted to the brain. This reduces phantom pain.

Saturday, August 21, 2010

Carole Palmer, Dustin Burnett and Brian Dean from Tufts University have published a list of dental myths in the journal Nutrition Today. The review article is geared toward helping people recognize the importance of oral health. I wrote previously about how oral health can affect heart health. Here are a few more things you should know about your teeth:

Prolonged exposure to sugar is worse than high amounts of sugar. In other words, sucking on a hard candy for an hour is worse for your teeth than chewing up a couple of sugar cubes. Not that dentists recommend munching on sugar cubes.

Teeth can be affected by osteoporosis. If osteoporosis is bad enough to weaken facial bones, it can lead to tooth loss.

Nutrition in pregnant women can affect the health of their babies' mouths. Poor nutrition, particularly during the second trimester when teeth are developing, can result in an increased tendency for the child to develop dental caries (cavities) later in life. There is also some evidence that nutritional deficiencies in the womb put children at risk for cleft palates and other oral deformities.

And while we’re on the subject of children, losing baby teeth to decay is not risk free. The infection that caused the cavity can spread through the jaw and damage the undescended adult teeth.

Thursday, August 19, 2010

When you breed a species to look like a chihuahua or a mastiff or every size and shape in between, you have to alter a lot of body features.Taryn Roberts and Paul Mcgreevy of the University of Sidney, and Michael Valenzuela of the University of New South Wales have found that body shape isn’t all that selective breeding has changed.It turns out that dog brains have been altered by breeding as well.

The researchers used magnetic resonance imaging (MRI) to look at a variety of canine brains and found some significant differences.In particular, the brains of short-snouted dogs like pugs are rotated forward by up to 15 degrees.The olfactory lobe (which processes smells) was also displaced compared to dogs with longer snouts.

Dogs have a remarkably flexible genome to be able to withstand such extreme changes and yet remain dogs. Valenzuela and the other researchers are interested in determining whether these differences in brain position translate to differences in brain function, and ultimately in behavior.

Wednesday, August 18, 2010

Airplanes require very long runways for landing. Birds, on the other hand, can land on telephone wires. Russ Tedrake from MIT and his student Rick Cory decided to see if they could make a plane act like a bird.

Regardless of whether planes are ascending or descending, they must keep their wings within only a few degrees of level. If they deviate too much from this angle, they go into a stall, which causes the plane to fall from the sky. Nobody wants that. But birds actually go into a purposeful stall each time they aim to land in a precise location. If engineers could precisely control stalling, then airplanes could be made to land on tiny areas just like birds. The trouble is that predicting exactly how air will flow around a plane during a stall has been extremely difficult. Tedrake and Cory developed their own mathematical model to do so.

So far, the team has successfully tested a foam prototype, for which Cory won Boeing’s 2010 Engineering Student of the Year award.

Here's a video clip of the model landing on a suspended string perch:

UPDATE: Because some people have not been able to view the video, here's a cartoon of the perching glider:

The glider is launched at a random initial speed that ranges anywhere from 6.0 to 8.5 meters per second (13.5-19 mph) and begins 3.5 meters (12 ft) away from the perch. It must then quickly decelerate to a near stop before making the point landing, by attaching a small hook under its belly to the perch. In order to slow down fast enough, the glider must orient its entire body to a high angle of attack, allowing it to exploit both viscous and pressure drag for braking. The entire maneuver last just a fraction of a second and is computer-controlled by varying the angle of the tail.

Tuesday, August 17, 2010

Plague, once known as ‘Black Death’ is caused by the bacterium Yersinia pestis.It spreads via infected fleas through many animal populations, including human. Among its common targets are prairie dogs, a type of burrowing rodent. What was not understood until recently was how the plague returns to decimate new prairie dog towns when there are no survivors to maintain it. In other words, where does the bacteria reside in between epidemics (or epizootics, in the case of animals)?Is it hiding in secondary hosts?In the soil?In puddles of fresh water?

Daniel Salkeld and his colleagues from Stanford and from the University of California Fullerton have found the plague reservoir:a carnivorous mouse called the grasshopper mouse (Onychomys leucogaster).These mice feast on insects, worms, scorpions and yes, dead prairie dogs.In so doing, they give infected fleas time to jump aboard the mice, which can then carry them to new, previously uninfected, prairie dog towns.

This result has implications for many diseases that may reside in rodent-infesting fleas, such as hantavirus, or anthrax.It’s not unusual for epidemics (or epizootics) to wax and wane mysteriously.Now researchers can be on the lookout for mice connecting one site of infection to the next.

Monday, August 16, 2010

William Provancher, the man who brought you the Active Handrest, plus Mark Fehlberg and Samuel Jensen-Segal, all from the University of Utah, have designed a robot that can go straight up walls. The Oscillating Climbing Robot, nicknamed ‘ROCR’, can climb any carpeted walls that provide access for its hook-like claws.

University of Utah mechanical engineer William Provancher watches as the efficient climbing robot he and colleagues developed scales a carpeted wall.

Credit: Mark Fehlberg, University of Utah

Although there are other robots that can climb walls, none have achieved the efficiency of ROCR. In other words, ROCR requires much less input energy to scale the same heights. In addition, at only 1.2 lbs and 18 inches from top to bottom, it’s compact enough to take to any desired location.

Climbing robots are in great demand to aid in inspection and maintenance of structures such as bridges. Obviously, a robot that requires a carpeted surface would have minimal real world use. However, Provancher is undaunted by this limitation:

While this robot eventually can be used for inspection, maintenance and surveillance, probably the greatest short-term potential is as a teaching tool or as a really cool toy.

Diabetics must carefully monitor their blood glucose levels via needle sticks, which sometimes must be performed many times each day. Some people use external insulin pumps, however, these are not generally connected to glucose monitors. Usually, the pumps must be preprogrammed by physicians, requiring patients to rigorously follow eating and exercise programs.

An internal monitor would eliminate the need for constant pricking. If connected to a pump, the entire system could allow continuous and virtually instantaneous insulin monitoring and control. There are some implantable glucose monitors, but none that last much longer than a week. In contrast, Gough’s device was successfully used in one pig for well over a year. The researchers look forward to starting human trials as soon as possible.

The tested device currently sends the glucose information to a wireless data recorder. The researchers anticipate one day sending the data to cell phones. For example, the data could be sent to a parent’s phone to alert her if her child needed attention during the night.

Saturday, August 14, 2010

Migratory birds experience differences in the amount and quality of sleep they get during different seasons. Ruth Benca and her colleagues from the University of Wisconsin-Madison have now shown that they also have decreased impulse control whilst in their migratory state.

Benca’s team has been studying the White-crowned Sparrow. This small bird spends 60% less time sleeping while migrating than at other times. Some specimens have been known to stay awake for up to two straight weeks. Nonetheless, it is capable of learning new behaviors, such as pecking a button to receive food, during periods of sleep deprivation. In contrast, during the migratory time period, it’s much more difficult for the birds to learn not to peck at a button, or not to perform some other action. They seem to have a decreased ability to withhold a response.

The scientists aren’t sure what is causing the loss of behavioral inhibition. It doesn’t appear to be purely a symptom of sleep deprivation because other types of learned behavior are not diminished.

As Benca states:

Whether the inability to inhibit pecking is related to a general failure of inhibition, a distorted sense of time, inattention to salient cues, or some other underlying mechanism is not entirely clear.

Thursday, August 12, 2010

From left to right, "healthy" man with a 33 inch (84 cm) waist; "overweight" man with a 45 inch (114 cm) waist; "obese" man with a 60 inch (152cm) waist.

The majority of obese individuals suffer from an assortment of metabolic disorders, including diabetes.However, a subset of obese people are surprisingly healthy despite being extremely overweight.In particular, some morbidly obese people are not insulin-resistant.Nuria Barbarroja led a team of scientists from Spain and Cambridge in discovering why not.

The researchers studied two groups of morbidly obese patients, one that was insulin-resistant and the other that was insulin-sensitive, like non-diabetic normal weight people.Although they had many similarities, where the groups of obese patients differed was in the expression of interleukin 1 alpha and interleukin 16, cytokines involved in immune response and in inflammation.The insulin-resistant individuals had much higher expression of both of these factors.

The researchers postulate that it is the inflammatory response that causes people to become diabetic.Most people suffer increased inflammation as they gain weight, but apparently some people don’t follow this normal pathway, and thus can remain relatively healthy, even while obese.Of course, there are other health issues associated with obesity besides diabetes, so it's still not recommended.

Wednesday, August 11, 2010

Ounce for ounce, spider silk is stronger than steel and tougher than Kevlar. There would be a myriad uses in the medical and material sciences for threads that are thinner than human hairs yet stronger than steel. Yet, collecting natural spider silk can be problematic as spiders make uncooperative life stock. Sang Yup Lee at the Korea Advanced Institute of Science and Technology (KAIST) and his collaborators, Professor Young Hwan Park at Seoul National University and Professor David Kaplan at Tufts University recently managed to overcome this problem by bioengineering silk.

The scientists got Escherichia coli bacteria to produce the spider silk protein. This was a daunting task in and of itself. For one thing, spider silk protein is a behemoth at 285 kilodaltons. To put that in perspective, ovalbumin, the main component of egg whites, weighs in at only 45 kilodaltons. Silk is also highly repetitive in nature, requiring enormous quantities of only a few different amino acids. In short, spider silk is not something bacteria like to waste their resources producing. With a bit of metabolic engineering and a vast pool of the appropriate raw materials, Lee and his team were able to coax the bacteria into producing the desired silk protein.

The resultant silk protein could be spun into artificial fiber comparable to spider dragline silk. The scientists expect to be able to use similar methods to create other kinds of artificial silk or silk-like materials. After all, spiders are known to produce at least five different kinds of silk, depending on whether they wish to support their body weight, capture prey, protect their young, or perform a host of other actions. Each of these silks would find wide use in human activities.

Tuesday, August 10, 2010

John James Audubon (1785-1851) may be the most famous wildlife illustrator of all time. Until recently, his first published illustration, of a running grouse, was missing. Historians had been hunting for that illustration for over half a century. The image of the grouse was finally tracked down by Robert Peck from the Academy of Natural Sciences, and by Eric Newman first author of an article in the Journal of the Early Republic.

In 1824, Audubon drew a running Heath hen (a subspecies of the Greater Prairie-Chicken) for use in a bank note. However, no bank notes of the time were found that contained that image. The team of researchers traced Audubon’s drawing to the engraver Gideon Fairman, and from him finally to some bank notes samples held in a private collection. The bank notes hadn’t been discovered earlier because they’d been made years later, not at the time Audubon handed his picture over to Fairman.

Finding the image was important to both historians and biologists. The former were able to better understand Audubon’s early emergence as the preeminent natural illustrator, and the latter had a glimpse of a bird that has been extinct since about the time Audubon drew it.

This is a detail of Audubon’s running grouse (Heath Hen) vignette from a Fairman Draper Underwood & Co. sample sheet. The image was discovered by an Audubon authority from the Academy of Natural Sciences in Philadelphia and by a numismatic historian from St. Louis.

Monday, August 9, 2010

It’s no surprise that excessive drinking results in memory loss during the binging.What’s more surprising is that teenagers who are heavy drinkers may be permanently affecting their memories even while sober.In particular, prospective memory (the ability to remember to carry out a future activity, such as show up for an appointment or return books to the library) appears to be damaged in teenaged drinkers.

Tom Hefferman of Northumbria University led a study testing the memory of 50 university students who did not use other substances (such as ecstasy, marijuana or tobacco) and had not had a drink in at least 48 hours.21 of the students were classified as binge drinkers, meaning that at least twice a week they drank 6 units of alcohol if women and 8 if men.One unit equals either a glass of wine or a beer.The other 29 participants were non-bingers.

All the volunteers were shown a ten-minute video clip of a shopping area.Prior to seeing the clip, they had been asked to perform specific actions when particular locations appeared on the video.The binge-drinkers remembered significantly fewer of the tasks than their non-binge drinking cohorts.Yet, when asked to evaluate themselves, the binge drinkers perceived themselves to have perfectly functioning memories.In other words, they did not realize that they were at all impaired.

It would be interesting to see whether binge drinking, if begun later in life, also affects prospective memory to the same degree.The authors of the study suspect that the damage would be much more severe in teens, since their brains are still developing.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.